java.lang.Object
- org.biojava.nbio.structure.align.client.StructureName

All Implemented Interfaces:

Serializable, Comparable<StructureName>, StructureIdentifier
```
public class StructureName
extends Object
implements Comparable<StructureName>, Serializable, StructureIdentifier
```
A utility class that makes working with names of structures, domains and ranges easier. Accepts a wide range of identifier formats, including ScopDomain, CathDomain, PDP domains, and SubstructureIdentifier residue ranges. Where possible, data is extracted from the input string. Otherwise, range information may be loaded from one of the factory classes: CathFactory,ScopFactory, etc.

See Also:

the name. e.g. 4hhb, 4hhb.A, d4hhba_, PDP:4HHBAa etc., Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class StructureName.Source

Field Summary

Fields
Modifier and Type Field Description

protected String chainName

protected String name

protected String pdbId

Constructor Summary

Constructors
Constructor Description

StructureName(String name)
Create a new StructureName from the given identifier, which may be a domain name, a substructure identifier, etc.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`compareTo(StructureName o)`	Orders identifiers lexicographically by PDB ID and then full Identifier
`boolean`	`equals(Object obj)`
`StructureIdentifier`	`getBaseIdentifier()`	StructureName wraps another StructureIdentifier.
`String`	`getChainId()`	Gets the chain ID, for structures where it is unique and well-defined.
`String`	`getIdentifier()`	Get the original form of the identifier
`String`	`getPdbId()`	Get the PDB ID for this name, if any.
`StructureName.Source`	`getSource()`
`static ScopDomain`	`guessScopDomain(String name, ScopDatabase scopDB)`	Guess a scop domain.
`int`	`hashCode()`
`boolean`	`isBioAssembly()`
`boolean`	`isCathID()`
`boolean`	`isEcodDomain()`
`boolean`	`isFile()`	Indicates that the identifier was determined to correspond to a file.
`boolean`	`isPdbId()`
`boolean`	`isPDPDomain()`
`boolean`	`isScopName()`
`boolean`	`isURL()`
`Structure`	`loadStructure(AtomCache cache)`	Loads a structure encompassing the structure identified.
`Structure`	`reduce(Structure input)`	Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
`SubstructureIdentifier`	`toCanonical()`	Convert to a canonical SubstructureIdentifier.
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - name
```
protected String name
```
  - pdbId
```
protected String pdbId
```
  - chainName
```
protected String chainName
```
- Constructor Detail
  - StructureName
```
public StructureName(String name)
```
    Create a new StructureName from the given identifier, which may be a domain name, a substructure identifier, etc.
    The source and PDB-Id are extracted at compile time, but fully interpreting the ID, which may require additional parsing or remote calls, is done lazily.
    The following sources are supported. Any may be prefixed by the source name followed by a colon (e.g. PDB:4HHB). In this case, that source will be used unequivocally. If no source is specified, StructureName will make a (usually reliable) guess as to which source was intended.
    
    PDBPDB identifier, optionally followed by chain and/or residue ranges. Internally represented by a SubstructureIdentifier; see that class for the full format specification. Examples: 4hhb, 4hhb.A, 4hhb.A:1-50.
    SCOP SCOP domain (or SCOPe, depending on the ScopFactory.getSCOP() version). Example: d1h6w.2
    PDP Protein Domain Parser domain. PDP domains are not guessed, making the PDP: prefix obligatory. Example: PDP:4HHBAa
    CATH Cath domains. Example: 1qvrC03
    URL Arbitrary URLs. Most common protocols are handled, including http://, ftp://, and file://. Some parsing information can be passed as custom query parameters. Example: http://www.rcsb.org/pdb/files/1B8G.pdb.gz
    FILE A file path. Supports relative paths and expands ~ to the user's home directory. Only existing files will be automatically detected; to refer to a potentially not-yet existing file, prepend the prefix. Internally represented as a URLIdentifier after path expansion. Example: ~/custom_protein.pdb
    ECOD ECOD domain. Example: e1lyw.1
    BIO Biological assembly. These are not guessed, making the BIO: prefix obligatory. Example: BIO:2ehz:1
    Parameters:
    
    name - An identifier string
    
    Throws:
    
    IllegalArgumentException - if the name has a recognizable source but is semantically invalid
- Method Detail
  - getPdbId
```
public String getPdbId()
                throws StructureException
```
    Get the PDB ID for this name, if any. Equivalent to toCanonical().getPdbId()
    
    Returns:
    
    The upper-case PDB Name, or null if not applicable
    
    Throws:
    
    StructureException - Wraps errors which occur when converting to canonical form
  - getChainId
```
public String getChainId()
```
    Gets the chain ID, for structures where it is unique and well-defined. May return '.' for multi-chain ranges, '_' for wildcard chains, or null if the information is unavailable.
    This method should only be used casually. For precise chainIds, it is better to use toCanonical() and iterate through the residue ranges.
    
    Returns:
  - getIdentifier
```
public String getIdentifier()
```
    Get the original form of the identifier
    
    Specified by:
    
    getIdentifier in interface StructureIdentifier
    
    Returns:
    
    The String form of this identifier
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - isScopName
```
public boolean isScopName()
```
  - isPDPDomain
```
public boolean isPDPDomain()
```
  - isCathID
```
public boolean isCathID()
```
  - isPdbId
```
public boolean isPdbId()
```
  - isURL
```
public boolean isURL()
```
  - isFile
```
public boolean isFile()
```
    Indicates that the identifier was determined to correspond to a file. Note that some file identifiers may also be valid URLs; in that case, the URL source is preferred.
    
    Returns:
  - isEcodDomain
```
public boolean isEcodDomain()
```
  - isBioAssembly
```
public boolean isBioAssembly()
```
  - getSource
```
public StructureName.Source getSource()
```
  - getBaseIdentifier
```
public StructureIdentifier getBaseIdentifier()
                                      throws StructureException
```
    StructureName wraps another StructureIdentifier. The type of the base identifier depends on the source. Most StructureName methods deligate to the base identifier.
    It is possible that future versions of StructureName might change the return type. Except for some specialized uses, it is probably better to create the correct type of identifier directly, rather than creating a StructureName and casting the result of this method.
    
    Returns:
    
    A Str
    
    Throws:
    
    StructureException - Wraps exceptions that may be thrown by individual implementations. For example, a SCOP identifier may require that the domain definitions be available for download.
  - toCanonical
```
public SubstructureIdentifier toCanonical()
                                   throws StructureException
```
    Description copied from interface: StructureIdentifier
    
    Convert to a canonical SubstructureIdentifier.
    This allows all domains to be converted to a standard format String.
    
    Specified by:
    
    toCanonical in interface StructureIdentifier
    
    Returns:
    
    A SubstructureIdentifier equivalent to this
    
    Throws:
    
    StructureException - Wraps exceptions that may be thrown by individual implementations. For example, a SCOP identifier may require that the domain definitions be available for download.
  - reduce
```
public Structure reduce(Structure input)
                 throws StructureException
```
    Description copied from interface: StructureIdentifier
    
    Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
    The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.
    
    Specified by:
    
    reduce in interface StructureIdentifier
    
    Parameters:
    
    input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.
    
    Returns:
    
    Throws:
    
    StructureException
    
    See Also:
    
    StructureTools.getReducedStructure(Structure, String)
  - loadStructure
```
public Structure loadStructure(AtomCache cache)
                        throws StructureException,
                               IOException
```
    Description copied from interface: StructureIdentifier
    
    Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input to StructureIdentifier.reduce(Structure). It is recommended that the most complete structure available be returned (e.g. the full PDB) to allow processing of unselected portions where appropriate.
    
    Specified by:
    
    loadStructure in interface StructureIdentifier
    
    Returns:
    
    A Structure containing at least the atoms identified by this, or null if Structures are not applicable.
    
    Throws:
    
    StructureException - For errors loading and parsing the structure
    
    IOException - Errors reading the structure from disk
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - compareTo
```
public int compareTo(StructureName o)
```
    Orders identifiers lexicographically by PDB ID and then full Identifier
    
    Specified by:
    
    compareTo in interface Comparable<StructureName>
  - guessScopDomain
```
public static ScopDomain guessScopDomain(String name,
                                         ScopDatabase scopDB)
```
    Guess a scop domain. If an exact match is found, return that.
    Otherwise, return the first scop domain found for the specified protein such that
    
    The chains match, or one of the chains is '_' or '.'.
    The domains match, or one of the domains is '_'.
    In some cases there may be several valid matches. In this case a warning will be logged.
    Parameters:
    
    name - SCOP domain name, or a guess thereof
    
    scopDB - SCOP domain provider
    
    Returns:
    
    The best match for name among the domains of scopDB, or null if none match.

Modifier and Type	Field	Description
`protected String`	`chainName`
`protected String`	`name`
`protected String`	`pdbId`

Class StructureName

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

name

pdbId

chainName

Constructor Detail

StructureName

Method Detail

getPdbId

getChainId

getIdentifier

toString

isScopName

isPDPDomain

isCathID

isPdbId

isURL

isFile

isEcodDomain

isBioAssembly

getSource

getBaseIdentifier

toCanonical

reduce

loadStructure

hashCode

equals

compareTo

guessScopDomain